OmniPath pathway annotation issue

[Lehoczky Zsombor]

Hi,

I'm a new to the OmniPath python library pypath, but even though I tried to carefully follow the steps described in the tutorials, I still can't get the module to return the pathway annotations.

I've attached an ipython notebook where I'm trying to run the module: download-annotations.html

I'm a windows user running the module in python 2.7. However, this doesn't look like a compatibility issue to me, as otherwise the module runs smoothly on my computer.

Please contact me if there's any kind of workaround to this problem. I hope this feedback was useful.

Best,

Zsombor Lehoczky

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Zsombor Lehoczky
Computational Biologist - LinkedIn

Turbine Ltd.
Mobile: + 36 30 634 7014

turbine.ai

[Dénes Türei]

Hi Zsombor,

Thanks for your feedback. Could you please confirm the version of your pypath is the recent? There were issues with these methods which I fixed in this https://github.com/saezlab/pypath/commit/88d3764f5e0ce13a2d12d6d08b7a57c346279f95 and the preceding few commits. If your module is older then you could just update and try if it works. If you already have the recent version but you have used these methods in the period when the downloads returned empty responses you need to delete the affected cache files. To test this you could turn off cache and run the download methods and see if they return empty dicts:

import pypath

with pypath.curl.cache_off():

  kegg = pypath.dataio.get_kegg()

  signor = pypath.dataio.signor_pathways()

I hope this helps.

Meanwhile I will check if these still work all right at me and also the other 2 pathway annotation methods.

Best wishes,

Denes

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Denes Turei, Ph.D.

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[Lehoczky Zsombor]

Hi Denes,

Thanks for your response. It was huge help.

I've been using v0.7.7, but now I upgraded to 0.7.22 and also tried to run with the cache turned off, and this made both Signor and KEGG pathways work.

As for the other two sources, they are -- as I understood from the documentation -- supposed to be integrated into the network and loaded when the network is initialized. If they seem to be working to you, then it might be that I've been using the wrong method for initializing the network. In either case, I'm thankful for any help to make them work.

Best regards,
Zsombor